Proteins

Proteins are composed of one or more peptide chains, folded into specific arrangements. Peptide chains are linear sequences of amino acids. The specific arrangements into which peptide chains join together or fold are largely determined by the amino acid sequences of the peptide chains. There are only 20 naturally occurring amino acids. There are nonpolar, polar uncharged, acidic, and basic amino acids. Consistent with other biomolecules, amino acids are asymmetric. They have a carboxyl group (COO) on one end and an amino group (NH3+) on the other.

Amino acids can link together through peptide bonds to form linear sequences (poly-peptide chains). In a peptide bond, the amino group of one amino acid links to the car-boxyl group of another amino acid. One or more polypeptide chains can fold together to form proteins. When notating the sequences of polypeptide chains, amino acid names are typically abbreviated by using three-letter codes.

Proteins generally fold to form the most stable structures possible. In addition to the primary amino acid sequence, other forces influence protein folding and structure, such as hydrogen bonds, hydrophobic interactions, electrostatic interactions, and attractive or repulsive (van der Waals) forces. Sometimes proteins are "helped" into their appropriate conformations by helper proteins called molecular chaperones. A peptide chain folded into its natural conformation is said to be in its native structure. Non-native structures can result when proteins are broken down, or denatured, by cooking, or by treatment with a strong base, such as urea.

The amino acid sequence is the primary (1°) structure of a protein. The secondary structure (2°) of a protein consists of the a-helix or ^-pleated sheet conformations formed by the polypeptide chains. Secondary structure largely depends on the amino acid sequences. The tertiary structure (3°) of a protein is the three-dimensional interactions of the secondary structure elements. Quaternary (4°) protein structure refers to the arrangement or interaction of two or more monomer subunits.

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